Starting phenix.real_space_refine on Sun Jul 5 08:41:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g6u_29783/07_2026/8g6u_29783.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6u_29783/07_2026/8g6u_29783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g6u_29783/07_2026/8g6u_29783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6u_29783/07_2026/8g6u_29783.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8g6u_29783/07_2026/8g6u_29783.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g6u_29783/07_2026/8g6u_29783.cif" model { file = "/net/cci-nas-00/data/ceres_data/8g6u_29783/07_2026/8g6u_29783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6u_29783/07_2026/8g6u_29783.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.014 sd= 0.602 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 16788 2.51 5 N 4377 2.21 5 O 5568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26871 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3510 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 23, 'TRANS': 419} Chain breaks: 3 Chain: "B" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "M" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "N" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "E" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3510 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 23, 'TRANS': 419} Chain breaks: 3 Chain: "F" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "G" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "H" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "O" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "P" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "I" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3510 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 23, 'TRANS': 419} Chain breaks: 3 Chain: "J" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "K" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "Q" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "R" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "S" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "U" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "k" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "s" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.06, per 1000 atoms: 0.23 Number of scatterers: 26871 At special positions: 0 Unit cell: (169.32, 156.04, 147.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 5568 8.00 N 4377 7.00 C 16788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.02 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.02 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.02 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN S 8 " - " MAN S 9 " " MAN S 10 " - " MAN S 11 " " MAN T 4 " - " MAN T 5 " " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN U 8 " - " MAN U 9 " " MAN Y 4 " - " MAN Y 5 " " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN a 8 " - " MAN a 9 " " MAN a 10 " - " MAN a 11 " " MAN b 4 " - " MAN b 5 " " MAN d 4 " - " MAN d 5 " " MAN d 5 " - " MAN d 6 " " MAN d 8 " - " MAN d 9 " " MAN h 4 " - " MAN h 5 " " MAN j 4 " - " MAN j 5 " " MAN j 5 " - " MAN j 6 " " MAN j 8 " - " MAN j 9 " " MAN j 10 " - " MAN j 11 " " MAN k 4 " - " MAN k 5 " " MAN n 4 " - " MAN n 5 " " MAN n 5 " - " MAN n 6 " " MAN n 8 " - " MAN n 9 " " MAN r 4 " - " MAN r 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " MAN S 7 " - " MAN S 8 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " MAN U 7 " - " MAN U 10 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 8 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " MAN d 7 " - " MAN d 10 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " MAN j 7 " - " MAN j 8 " " BMA k 3 " - " MAN k 4 " " BMA n 3 " - " MAN n 4 " " MAN n 7 " - " MAN n 10 " " BMA r 3 " - " MAN r 4 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA S 3 " - " MAN S 7 " " MAN S 7 " - " MAN S 10 " " BMA T 3 " - " MAN T 6 " " BMA U 3 " - " MAN U 7 " " MAN U 7 " - " MAN U 8 " " BMA Y 3 " - " MAN Y 6 " " BMA Z 3 " - " MAN Z 5 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 10 " " BMA b 3 " - " MAN b 6 " " BMA d 3 " - " MAN d 7 " " MAN d 7 " - " MAN d 8 " " BMA h 3 " - " MAN h 6 " " BMA i 3 " - " MAN i 5 " " BMA j 3 " - " MAN j 7 " " MAN j 7 " - " MAN j 10 " " BMA k 3 " - " MAN k 6 " " BMA n 3 " - " MAN n 7 " " MAN n 7 " - " MAN n 8 " " BMA r 3 " - " MAN r 6 " " BMA s 3 " - " MAN s 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN A 448 " " NAG 1 1 " - " ASN E 448 " " NAG 2 1 " - " ASN I 448 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 187 " " NAG A 604 " - " ASN A 295 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 355 " " NAG A 607 " - " ASN A 411 " " NAG A 608 " - " ASN A 465 " " NAG A 609 " - " ASN A 392 " " NAG B 700 " - " ASN B 611 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 625 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 187 " " NAG E 604 " - " ASN E 295 " " NAG E 605 " - " ASN E 301 " " NAG E 606 " - " ASN E 355 " " NAG E 607 " - " ASN E 411 " " NAG E 608 " - " ASN E 465 " " NAG E 609 " - " ASN E 392 " " NAG F 700 " - " ASN F 611 " " NAG F 701 " - " ASN F 616 " " NAG F 702 " - " ASN F 625 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 160 " " NAG I 603 " - " ASN I 187 " " NAG I 604 " - " ASN I 295 " " NAG I 605 " - " ASN I 301 " " NAG I 606 " - " ASN I 355 " " NAG I 607 " - " ASN I 411 " " NAG I 608 " - " ASN I 465 " " NAG I 609 " - " ASN I 392 " " NAG J 700 " - " ASN J 611 " " NAG J 701 " - " ASN J 616 " " NAG J 702 " - " ASN J 625 " " NAG S 1 " - " ASN A 234 " " NAG T 1 " - " ASN A 276 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 197 " " NAG Y 1 " - " ASN A 262 " " NAG Z 1 " - " ASN B 637 " " NAG a 1 " - " ASN E 234 " " NAG b 1 " - " ASN E 276 " " NAG c 1 " - " ASN E 156 " " NAG d 1 " - " ASN E 332 " " NAG e 1 " - " ASN E 386 " " NAG f 1 " - " ASN A 156 " " NAG g 1 " - " ASN E 197 " " NAG h 1 " - " ASN E 262 " " NAG i 1 " - " ASN F 637 " " NAG j 1 " - " ASN I 234 " " NAG k 1 " - " ASN I 276 " " NAG l 1 " - " ASN I 156 " " NAG m 1 " - " ASN I 289 " " NAG n 1 " - " ASN I 332 " " NAG o 1 " - " ASN I 386 " " NAG p 1 " - " ASN I 197 " " NAG q 1 " - " ASN I 130 " " NAG r 1 " - " ASN I 262 " " NAG s 1 " - " ASN J 637 " " NAG t 1 " - " ASN A 130 " " NAG u 1 " - " ASN E 130 " " NAG v 1 " - " ASN A 289 " " NAG w 1 " - " ASN E 289 " " NAG x 1 " - " ASN A 241 " " NAG y 1 " - " ASN E 241 " " NAG z 1 " - " ASN I 241 " Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.1 seconds 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5718 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 57 sheets defined 15.2% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.860A pdb=" N GLU A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.640A pdb=" N MET A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.937A pdb=" N ASN A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 537 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.796A pdb=" N ILE B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.902A pdb=" N THR C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.665A pdb=" N PHE D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 100D through 100H Processing helix chain 'N' and resid 79 through 84 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 334 through 353 removed outlier: 3.860A pdb=" N GLU E 351 " --> pdb=" O ASN E 347 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.641A pdb=" N MET E 373 " --> pdb=" O PRO E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 481 removed outlier: 3.936A pdb=" N ASN E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 537 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.795A pdb=" N ILE F 622 " --> pdb=" O THR F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.902A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.665A pdb=" N PHE H 83 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100D through 100H Processing helix chain 'P' and resid 79 through 84 Processing helix chain 'I' and resid 96 through 98 No H-bonds generated for 'chain 'I' and resid 96 through 98' Processing helix chain 'I' and resid 99 through 117 Processing helix chain 'I' and resid 334 through 353 removed outlier: 3.860A pdb=" N GLU I 351 " --> pdb=" O ASN I 347 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS I 352 " --> pdb=" O LYS I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.640A pdb=" N MET I 373 " --> pdb=" O PRO I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 481 removed outlier: 3.936A pdb=" N ASN I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 537 Processing helix chain 'J' and resid 569 through 596 Processing helix chain 'J' and resid 618 through 625 removed outlier: 3.796A pdb=" N ILE J 622 " --> pdb=" O THR J 618 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 661 Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.903A pdb=" N THR K 87 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.666A pdb=" N PHE L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 87 Processing helix chain 'Q' and resid 100D through 100H Processing helix chain 'R' and resid 79 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.093A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 155 through 162 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.545A pdb=" N ILE A 271 " --> pdb=" O HIS A 287 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 417 removed outlier: 3.592A pdb=" N CYS A 331 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.862A pdb=" N GLU C 10 " --> pdb=" O SER C 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.990A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLN C 50 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL C 35 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP C 52 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N TYR C 33 " --> pdb=" O TRP C 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 100E through 100F Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.722A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.617A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR D 72 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.578A pdb=" N GLN M 5 " --> pdb=" O SER M 23 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 11 through 12 removed outlier: 4.253A pdb=" N THR M 107 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR M 90 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL M 109 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA M 93 " --> pdb=" O THR M 35 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR M 35 " --> pdb=" O ALA M 93 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE M 48 " --> pdb=" O TRP M 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 11 through 12 removed outlier: 4.253A pdb=" N THR M 107 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR M 90 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL M 109 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG M 100 " --> pdb=" O PHE M 100K" (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE M 100K" --> pdb=" O ARG M 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 45 through 46 removed outlier: 3.559A pdb=" N HIS N 89 " --> pdb=" O GLN N 34 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR N 36 " --> pdb=" O TYR N 87 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 494 through 499 Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.092A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 155 through 162 Processing sheet with id=AC6, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AC7, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.544A pdb=" N ILE E 271 " --> pdb=" O HIS E 287 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 414 through 417 removed outlier: 3.592A pdb=" N CYS E 331 " --> pdb=" O ILE E 416 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS E 296 " --> pdb=" O CYS E 445 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AD1, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.863A pdb=" N GLU G 10 " --> pdb=" O SER G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.990A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN G 50 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL G 35 " --> pdb=" O GLN G 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP G 52 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N TYR G 33 " --> pdb=" O TRP G 52 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 100E through 100F Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.721A pdb=" N ILE H 48 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 19 through 24 removed outlier: 3.617A pdb=" N PHE H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR H 72 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.579A pdb=" N GLN O 5 " --> pdb=" O SER O 23 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 11 through 12 removed outlier: 4.253A pdb=" N THR O 107 " --> pdb=" O TYR O 90 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR O 90 " --> pdb=" O THR O 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL O 109 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA O 88 " --> pdb=" O VAL O 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA O 93 " --> pdb=" O THR O 35 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR O 35 " --> pdb=" O ALA O 93 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE O 48 " --> pdb=" O TRP O 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 11 through 12 removed outlier: 4.253A pdb=" N THR O 107 " --> pdb=" O TYR O 90 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR O 90 " --> pdb=" O THR O 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL O 109 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA O 88 " --> pdb=" O VAL O 109 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG O 100 " --> pdb=" O PHE O 100K" (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE O 100K" --> pdb=" O ARG O 100 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 45 through 46 removed outlier: 3.559A pdb=" N HIS P 89 " --> pdb=" O GLN P 34 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR P 36 " --> pdb=" O TYR P 87 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR P 87 " --> pdb=" O TYR P 36 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 494 through 499 Processing sheet with id=AE4, first strand: chain 'I' and resid 45 through 47 removed outlier: 4.092A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 92 through 94 Processing sheet with id=AE6, first strand: chain 'I' and resid 155 through 162 Processing sheet with id=AE7, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AE8, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.544A pdb=" N ILE I 271 " --> pdb=" O HIS I 287 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR I 357 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE I 468 " --> pdb=" O THR I 357 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 414 through 417 removed outlier: 3.592A pdb=" N CYS I 331 " --> pdb=" O ILE I 416 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS I 296 " --> pdb=" O CYS I 445 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 304 through 308 Processing sheet with id=AF2, first strand: chain 'I' and resid 423 through 424 Processing sheet with id=AF3, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.863A pdb=" N GLU K 10 " --> pdb=" O SER K 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.990A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN K 50 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL K 35 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP K 52 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N TYR K 33 " --> pdb=" O TRP K 52 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 100E through 100F Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.722A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.616A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 4 through 7 removed outlier: 3.577A pdb=" N GLN Q 5 " --> pdb=" O SER Q 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 11 through 12 removed outlier: 4.254A pdb=" N THR Q 107 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR Q 90 " --> pdb=" O THR Q 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL Q 109 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA Q 88 " --> pdb=" O VAL Q 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA Q 93 " --> pdb=" O THR Q 35 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR Q 35 " --> pdb=" O ALA Q 93 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE Q 48 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 11 through 12 removed outlier: 4.254A pdb=" N THR Q 107 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR Q 90 " --> pdb=" O THR Q 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL Q 109 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA Q 88 " --> pdb=" O VAL Q 109 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG Q 100 " --> pdb=" O PHE Q 100K" (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE Q 100K" --> pdb=" O ARG Q 100 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'R' and resid 45 through 46 removed outlier: 3.560A pdb=" N HIS R 89 " --> pdb=" O GLN R 34 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR R 36 " --> pdb=" O TYR R 87 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR R 87 " --> pdb=" O TYR R 36 " (cutoff:3.500A) 711 hydrogen bonds defined for protein. 1836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.62 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7692 1.34 - 1.46: 5853 1.46 - 1.58: 13698 1.58 - 1.70: 6 1.70 - 1.82: 186 Bond restraints: 27435 Sorted by residual: bond pdb=" N LEU F 544 " pdb=" CA LEU F 544 " ideal model delta sigma weight residual 1.457 1.507 -0.050 1.29e-02 6.01e+03 1.49e+01 bond pdb=" N LEU B 544 " pdb=" CA LEU B 544 " ideal model delta sigma weight residual 1.457 1.507 -0.049 1.29e-02 6.01e+03 1.46e+01 bond pdb=" N LEU J 544 " pdb=" CA LEU J 544 " ideal model delta sigma weight residual 1.457 1.507 -0.049 1.29e-02 6.01e+03 1.45e+01 bond pdb=" C1 NAG E 603 " pdb=" O5 NAG E 603 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C1 NAG I 603 " pdb=" O5 NAG I 603 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 27430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 36195 2.62 - 5.24: 849 5.24 - 7.86: 177 7.86 - 10.48: 30 10.48 - 13.10: 12 Bond angle restraints: 37263 Sorted by residual: angle pdb=" C PRO O 41 " pdb=" CA PRO O 41 " pdb=" CB PRO O 41 " ideal model delta sigma weight residual 111.56 124.66 -13.10 1.65e+00 3.67e-01 6.30e+01 angle pdb=" C PRO Q 41 " pdb=" CA PRO Q 41 " pdb=" CB PRO Q 41 " ideal model delta sigma weight residual 111.56 124.65 -13.09 1.65e+00 3.67e-01 6.29e+01 angle pdb=" C PRO M 41 " pdb=" CA PRO M 41 " pdb=" CB PRO M 41 " ideal model delta sigma weight residual 111.56 124.64 -13.08 1.65e+00 3.67e-01 6.28e+01 angle pdb=" N ARG F 542 " pdb=" CA ARG F 542 " pdb=" C ARG F 542 " ideal model delta sigma weight residual 107.49 119.28 -11.79 1.74e+00 3.30e-01 4.59e+01 angle pdb=" N ARG B 542 " pdb=" CA ARG B 542 " pdb=" C ARG B 542 " ideal model delta sigma weight residual 107.49 119.27 -11.78 1.74e+00 3.30e-01 4.58e+01 ... (remaining 37258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 13322 17.90 - 35.81: 1144 35.81 - 53.71: 291 53.71 - 71.62: 60 71.62 - 89.52: 30 Dihedral angle restraints: 14847 sinusoidal: 5922 harmonic: 8925 Sorted by residual: dihedral pdb=" CB CYS R 23 " pdb=" SG CYS R 23 " pdb=" SG CYS R 88 " pdb=" CB CYS R 88 " ideal model delta sinusoidal sigma weight residual -86.00 -3.23 -82.77 1 1.00e+01 1.00e-02 8.39e+01 dihedral pdb=" CB CYS P 23 " pdb=" SG CYS P 23 " pdb=" SG CYS P 88 " pdb=" CB CYS P 88 " ideal model delta sinusoidal sigma weight residual -86.00 -3.28 -82.72 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 88 " pdb=" CB CYS N 88 " ideal model delta sinusoidal sigma weight residual -86.00 -3.28 -82.72 1 1.00e+01 1.00e-02 8.38e+01 ... (remaining 14844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 4641 0.168 - 0.337: 45 0.337 - 0.505: 6 0.505 - 0.674: 3 0.674 - 0.842: 12 Chirality restraints: 4707 Sorted by residual: chirality pdb=" C1 NAG 2 1 " pdb=" ND2 ASN I 448 " pdb=" C2 NAG 2 1 " pdb=" O5 NAG 2 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" C1 NAG 0 1 " pdb=" ND2 ASN A 448 " pdb=" C2 NAG 0 1 " pdb=" O5 NAG 0 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.76e+01 chirality pdb=" C1 NAG 1 1 " pdb=" ND2 ASN E 448 " pdb=" C2 NAG 1 1 " pdb=" O5 NAG 1 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.74e+01 ... (remaining 4704 not shown) Planarity restraints: 4518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 386 " 0.011 2.00e-02 2.50e+03 6.99e-02 6.10e+01 pdb=" CG ASN A 386 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN A 386 " 0.078 2.00e-02 2.50e+03 pdb=" ND2 ASN A 386 " -0.088 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 386 " -0.011 2.00e-02 2.50e+03 6.96e-02 6.05e+01 pdb=" CG ASN E 386 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN E 386 " -0.078 2.00e-02 2.50e+03 pdb=" ND2 ASN E 386 " 0.087 2.00e-02 2.50e+03 pdb=" C1 NAG e 1 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 386 " -0.011 2.00e-02 2.50e+03 6.77e-02 5.73e+01 pdb=" CG ASN I 386 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN I 386 " -0.076 2.00e-02 2.50e+03 pdb=" ND2 ASN I 386 " 0.084 2.00e-02 2.50e+03 pdb=" C1 NAG o 1 " -0.069 2.00e-02 2.50e+03 ... (remaining 4515 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 278 2.54 - 3.13: 20837 3.13 - 3.72: 38379 3.72 - 4.31: 55133 4.31 - 4.90: 92275 Nonbonded interactions: 206902 Sorted by model distance: nonbonded pdb=" O GLN F 543 " pdb=" O LEU F 544 " model vdw 1.945 3.040 nonbonded pdb=" O GLN B 543 " pdb=" O LEU B 544 " model vdw 1.945 3.040 nonbonded pdb=" O GLN J 543 " pdb=" O LEU J 544 " model vdw 1.946 3.040 nonbonded pdb=" N GLU B 620 " pdb=" OE1 GLU B 620 " model vdw 2.056 3.120 nonbonded pdb=" N GLU J 620 " pdb=" OE1 GLU J 620 " model vdw 2.056 3.120 ... (remaining 206897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain 'V' selection = chain 'X' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'S' and (resid 2 or resid 5 through 11)) selection = (chain 'U' and (resid 1 or resid 4 through 10)) selection = (chain 'a' and (resid 2 or resid 5 through 11)) selection = (chain 'd' and (resid 1 or resid 4 through 10)) selection = (chain 'j' and (resid 2 or resid 5 through 11)) selection = (chain 'n' and (resid 1 or resid 4 through 10)) } ncs_group { reference = chain 'T' selection = chain 'Y' selection = chain 'b' selection = chain 'h' selection = chain 'k' selection = chain 'r' } ncs_group { reference = chain 'Z' selection = chain 'i' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 24.360 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 27672 Z= 0.295 Angle : 1.129 23.078 37929 Z= 0.527 Chirality : 0.070 0.842 4707 Planarity : 0.007 0.097 4446 Dihedral : 14.743 89.521 8994 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.98 % Allowed : 7.56 % Favored : 91.45 % Rotamer: Outliers : 3.79 % Allowed : 1.93 % Favored : 94.28 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.15), residues: 3054 helix: 1.65 (0.27), residues: 381 sheet: -0.19 (0.19), residues: 795 loop : -2.04 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 45 TYR 0.019 0.001 TYR R 49 PHE 0.013 0.001 PHE E 288 TRP 0.019 0.001 TRP I 69 HIS 0.003 0.001 HIS I 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.30 (27435) covalent geometry : angle 0.99315 / 0.50 (37263) SS BOND : bond 0.00470 / 0.33 ( 45) SS BOND : angle 1.54818 / 1.21 ( 90) hydrogen bonds : bond 0.22036 / 14.53 ( 708) hydrogen bonds : angle 8.41360 / 5.81 ( 1836) link_ALPHA1-2 : bond 0.00476 / 0.29 ( 27) link_ALPHA1-2 : angle 1.59671 / 1.15 ( 81) link_ALPHA1-3 : bond 0.00352 / 0.23 ( 21) link_ALPHA1-3 : angle 1.98881 / 1.42 ( 63) link_ALPHA1-6 : bond 0.00367 / 0.23 ( 21) link_ALPHA1-6 : angle 1.85561 / 1.31 ( 63) link_BETA1-4 : bond 0.00711 / 0.45 ( 51) link_BETA1-4 : angle 2.16681 / 1.47 ( 153) link_NAG-ASN : bond 0.00879 / 0.52 ( 72) link_NAG-ASN : angle 6.80255 / 5.11 ( 216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 612 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 545 LEU cc_start: 0.4963 (OUTLIER) cc_final: 0.4601 (tp) REVERT: C 66 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.8032 (ttt-90) REVERT: G 13 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8380 (mmmt) REVERT: H 4 MET cc_start: 0.7499 (ttm) cc_final: 0.7054 (ttm) REVERT: H 88 CYS cc_start: 0.5394 (p) cc_final: 0.5050 (p) REVERT: O 100 MET cc_start: 0.8126 (mpp) cc_final: 0.7355 (mpp) REVERT: I 103 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7711 (tp40) REVERT: I 107 ASP cc_start: 0.8100 (m-30) cc_final: 0.7884 (m-30) REVERT: L 24 ARG cc_start: 0.7848 (ttm110) cc_final: 0.7642 (ttm110) REVERT: Q 100 TYR cc_start: 0.7833 (m-10) cc_final: 0.7221 (m-10) outliers start: 102 outliers final: 31 residues processed: 662 average time/residue: 0.1747 time to fit residues: 186.6040 Evaluate side-chains 511 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 476 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 503 ARG Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 650 GLN Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain P residue 95 SER Chi-restraints excluded: chain I residue 103 GLN Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 474 ASP Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 503 ARG Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 650 GLN Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain R residue 95 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN A 229 ASN B 540 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN D 6 GLN M 64 ASN E 229 ASN F 540 GLN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 641 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 64 ASN I 229 ASN J 540 GLN ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 641 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 64 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.164022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.119886 restraints weight = 42321.593| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.27 r_work: 0.3399 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 27672 Z= 0.224 Angle : 0.889 20.971 37929 Z= 0.411 Chirality : 0.052 0.485 4707 Planarity : 0.006 0.151 4446 Dihedral : 7.426 105.206 3445 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.83 % Favored : 91.39 % Rotamer: Outliers : 3.05 % Allowed : 12.00 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.15), residues: 3054 helix: 1.38 (0.26), residues: 411 sheet: -0.40 (0.17), residues: 873 loop : -1.92 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 542 TYR 0.015 0.002 TYR I 39 PHE 0.018 0.002 PHE I 288 TRP 0.018 0.002 TRP R 91 HIS 0.003 0.001 HIS I 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (27435) covalent geometry : angle 0.77397 / 0.39 (37263) SS BOND : bond 0.00929 / 0.54 ( 45) SS BOND : angle 1.36418 / 0.99 ( 90) hydrogen bonds : bond 0.04720 / 3.16 ( 708) hydrogen bonds : angle 6.26858 / 4.33 ( 1836) link_ALPHA1-2 : bond 0.00377 / 0.24 ( 27) link_ALPHA1-2 : angle 1.98836 / 1.42 ( 81) link_ALPHA1-3 : bond 0.00318 / 0.20 ( 21) link_ALPHA1-3 : angle 1.78544 / 1.28 ( 63) link_ALPHA1-6 : bond 0.00449 / 0.29 ( 21) link_ALPHA1-6 : angle 1.60286 / 1.13 ( 63) link_BETA1-4 : bond 0.00521 / 0.36 ( 51) link_BETA1-4 : angle 2.24453 / 1.51 ( 153) link_NAG-ASN : bond 0.00657 / 0.41 ( 72) link_NAG-ASN : angle 5.27517 / 3.83 ( 216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 515 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 652 GLN cc_start: 0.7789 (tp40) cc_final: 0.7580 (tp40) REVERT: D 24 ARG cc_start: 0.8542 (ttm110) cc_final: 0.7902 (ttm110) REVERT: E 368 ASP cc_start: 0.7606 (m-30) cc_final: 0.7287 (m-30) REVERT: E 377 ASN cc_start: 0.8537 (p0) cc_final: 0.8288 (p0) REVERT: F 652 GLN cc_start: 0.8034 (tp40) cc_final: 0.7806 (tp40) REVERT: G 86 ASP cc_start: 0.9006 (m-30) cc_final: 0.8771 (m-30) REVERT: P 35 TRP cc_start: 0.7024 (m100) cc_final: 0.6536 (m100) REVERT: I 103 GLN cc_start: 0.8499 (mm110) cc_final: 0.8038 (mm-40) REVERT: I 104 MET cc_start: 0.9096 (ttt) cc_final: 0.8831 (ttt) REVERT: I 377 ASN cc_start: 0.8302 (p0) cc_final: 0.8093 (p0) REVERT: J 640 SER cc_start: 0.8797 (OUTLIER) cc_final: 0.8558 (m) REVERT: K 66 ARG cc_start: 0.8523 (mtp85) cc_final: 0.8198 (ttt90) REVERT: L 24 ARG cc_start: 0.8360 (ttm110) cc_final: 0.8104 (ttm110) REVERT: L 81 GLU cc_start: 0.8566 (pm20) cc_final: 0.8346 (pm20) REVERT: L 90 GLN cc_start: 0.9369 (pp30) cc_final: 0.9020 (pp30) REVERT: Q 74 SER cc_start: 0.7537 (p) cc_final: 0.7177 (m) outliers start: 82 outliers final: 53 residues processed: 573 average time/residue: 0.1609 time to fit residues: 149.3431 Evaluate side-chains 506 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 452 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain O residue 41 PRO Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 640 SER Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain Q residue 41 PRO Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 95 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 204 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 146 optimal weight: 0.0970 chunk 64 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 296 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN F 641 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN K 43 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 26 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.160264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.115913 restraints weight = 42366.371| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.26 r_work: 0.3338 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27672 Z= 0.187 Angle : 0.790 15.622 37929 Z= 0.368 Chirality : 0.049 0.434 4707 Planarity : 0.006 0.152 4446 Dihedral : 5.551 56.169 3375 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.89 % Favored : 91.49 % Rotamer: Outliers : 3.83 % Allowed : 16.09 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.15), residues: 3054 helix: 1.51 (0.26), residues: 420 sheet: -0.53 (0.17), residues: 912 loop : -1.90 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 20 TYR 0.020 0.002 TYR A 384 PHE 0.014 0.002 PHE F 592 TRP 0.015 0.001 TRP R 91 HIS 0.005 0.001 HIS I 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (27435) covalent geometry : angle 0.70033 / 0.35 (37263) SS BOND : bond 0.00814 / 0.55 ( 45) SS BOND : angle 1.26379 / 0.88 ( 90) hydrogen bonds : bond 0.04715 / 3.15 ( 708) hydrogen bonds : angle 5.79507 / 3.98 ( 1836) link_ALPHA1-2 : bond 0.00443 / 0.28 ( 27) link_ALPHA1-2 : angle 1.67835 / 1.18 ( 81) link_ALPHA1-3 : bond 0.00456 / 0.29 ( 21) link_ALPHA1-3 : angle 1.78784 / 1.27 ( 63) link_ALPHA1-6 : bond 0.00397 / 0.25 ( 21) link_ALPHA1-6 : angle 1.53159 / 1.08 ( 63) link_BETA1-4 : bond 0.00492 / 0.34 ( 51) link_BETA1-4 : angle 1.94066 / 1.33 ( 153) link_NAG-ASN : bond 0.00656 / 0.39 ( 72) link_NAG-ASN : angle 4.35426 / 3.18 ( 216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 493 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8413 (tp40) REVERT: A 107 ASP cc_start: 0.8750 (m-30) cc_final: 0.8248 (m-30) REVERT: A 125 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8857 (mp) REVERT: A 161 MET cc_start: 0.8858 (tpp) cc_final: 0.8523 (tpt) REVERT: A 368 ASP cc_start: 0.7586 (m-30) cc_final: 0.7237 (m-30) REVERT: A 373 MET cc_start: 0.8466 (mmt) cc_final: 0.8117 (mmt) REVERT: B 545 LEU cc_start: 0.5008 (OUTLIER) cc_final: 0.4773 (tp) REVERT: C 10 GLU cc_start: 0.8535 (pm20) cc_final: 0.8136 (pm20) REVERT: C 100 ARG cc_start: 0.8206 (mtp-110) cc_final: 0.7488 (ttt180) REVERT: D 24 ARG cc_start: 0.8586 (ttm110) cc_final: 0.8293 (ttm110) REVERT: M 100 ARG cc_start: 0.8375 (ttt90) cc_final: 0.8085 (tpt-90) REVERT: N 35 TRP cc_start: 0.7464 (m100) cc_final: 0.6885 (m100) REVERT: N 47 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8176 (mm) REVERT: N 49 TYR cc_start: 0.7936 (p90) cc_final: 0.7640 (p90) REVERT: E 168 LYS cc_start: 0.9412 (mmmt) cc_final: 0.9094 (mmtp) REVERT: E 368 ASP cc_start: 0.7596 (m-30) cc_final: 0.7327 (m-30) REVERT: E 377 ASN cc_start: 0.8715 (p0) cc_final: 0.8446 (p0) REVERT: F 652 GLN cc_start: 0.8167 (tp40) cc_final: 0.7851 (tp40) REVERT: G 28 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8484 (p0) REVERT: G 86 ASP cc_start: 0.9042 (m-30) cc_final: 0.8820 (m-30) REVERT: O 29 MET cc_start: 0.6103 (tpt) cc_final: 0.5743 (tpp) REVERT: O 100 MET cc_start: 0.8259 (mpp) cc_final: 0.7528 (mpp) REVERT: P 35 TRP cc_start: 0.7303 (m100) cc_final: 0.6964 (m100) REVERT: I 103 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8136 (mm-40) REVERT: I 104 MET cc_start: 0.9125 (ttt) cc_final: 0.8882 (ttt) REVERT: I 107 ASP cc_start: 0.8831 (m-30) cc_final: 0.8471 (m-30) REVERT: I 368 ASP cc_start: 0.7503 (m-30) cc_final: 0.7264 (m-30) REVERT: I 377 ASN cc_start: 0.8576 (p0) cc_final: 0.8297 (p0) REVERT: K 13 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8529 (mtpp) REVERT: K 100 ARG cc_start: 0.8232 (mtp-110) cc_final: 0.7594 (ttt180) REVERT: L 24 ARG cc_start: 0.8428 (ttm110) cc_final: 0.8003 (ttm110) REVERT: Q 74 SER cc_start: 0.7643 (p) cc_final: 0.7314 (m) REVERT: Q 97 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7138 (ttp80) REVERT: R 97 SER cc_start: 0.9348 (t) cc_final: 0.9066 (t) outliers start: 103 outliers final: 64 residues processed: 560 average time/residue: 0.1628 time to fit residues: 149.2056 Evaluate side-chains 530 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 461 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain M residue 41 PRO Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 41 PRO Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain J residue 529 THR Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain Q residue 41 PRO Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 33 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 227 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 253 optimal weight: 0.0980 chunk 134 optimal weight: 0.5980 chunk 256 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 290 optimal weight: 0.4980 chunk 284 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 HIS ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN M 99 GLN N 52 GLN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 ASN K 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.163434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119163 restraints weight = 41937.735| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.24 r_work: 0.3383 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27672 Z= 0.135 Angle : 0.748 20.457 37929 Z= 0.344 Chirality : 0.049 0.997 4707 Planarity : 0.005 0.152 4446 Dihedral : 5.375 59.746 3369 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.83 % Favored : 91.62 % Rotamer: Outliers : 3.64 % Allowed : 18.28 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.15), residues: 3054 helix: 1.30 (0.26), residues: 435 sheet: -0.61 (0.17), residues: 906 loop : -1.76 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 476 TYR 0.012 0.001 TYR K 47 PHE 0.009 0.001 PHE P 67 TRP 0.010 0.001 TRP A 96 HIS 0.002 0.001 HIS G 100F Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (27435) covalent geometry : angle 0.65798 / 0.32 (37263) SS BOND : bond 0.00509 / 0.36 ( 45) SS BOND : angle 1.28069 / 0.89 ( 90) hydrogen bonds : bond 0.04111 / 2.77 ( 708) hydrogen bonds : angle 5.48844 / 3.77 ( 1836) link_ALPHA1-2 : bond 0.00383 / 0.24 ( 27) link_ALPHA1-2 : angle 1.64515 / 1.16 ( 81) link_ALPHA1-3 : bond 0.00396 / 0.25 ( 21) link_ALPHA1-3 : angle 1.69723 / 1.22 ( 63) link_ALPHA1-6 : bond 0.00373 / 0.24 ( 21) link_ALPHA1-6 : angle 1.48833 / 1.05 ( 63) link_BETA1-4 : bond 0.00427 / 0.29 ( 51) link_BETA1-4 : angle 1.69539 / 1.16 ( 153) link_NAG-ASN : bond 0.00590 / 0.35 ( 72) link_NAG-ASN : angle 4.28905 / 3.21 ( 216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 497 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8730 (tp40) cc_final: 0.8132 (mm-40) REVERT: A 107 ASP cc_start: 0.8793 (m-30) cc_final: 0.8258 (m-30) REVERT: A 161 MET cc_start: 0.8869 (tpp) cc_final: 0.8521 (tpt) REVERT: A 368 ASP cc_start: 0.7506 (m-30) cc_final: 0.7073 (m-30) REVERT: B 545 LEU cc_start: 0.5189 (OUTLIER) cc_final: 0.4810 (tp) REVERT: C 100 ARG cc_start: 0.8124 (mtp-110) cc_final: 0.7683 (ttt90) REVERT: M 97 ARG cc_start: 0.8285 (ttp80) cc_final: 0.8077 (ttp80) REVERT: M 100 ARG cc_start: 0.8463 (ttt90) cc_final: 0.8200 (tpt-90) REVERT: N 35 TRP cc_start: 0.7515 (m100) cc_final: 0.7025 (m100) REVERT: N 47 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8309 (mm) REVERT: N 49 TYR cc_start: 0.7929 (p90) cc_final: 0.7667 (p90) REVERT: E 103 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7569 (mp10) REVERT: E 168 LYS cc_start: 0.9421 (mmmt) cc_final: 0.9134 (mmtp) REVERT: E 368 ASP cc_start: 0.7626 (m-30) cc_final: 0.7217 (m-30) REVERT: E 377 ASN cc_start: 0.8702 (p0) cc_final: 0.8462 (p0) REVERT: F 652 GLN cc_start: 0.8263 (tp40) cc_final: 0.7968 (tp40) REVERT: G 28 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8485 (p0) REVERT: G 86 ASP cc_start: 0.8938 (m-30) cc_final: 0.8673 (m-30) REVERT: G 100 ARG cc_start: 0.8232 (mtp-110) cc_final: 0.7572 (ttt90) REVERT: H 4 MET cc_start: 0.8240 (ttt) cc_final: 0.7978 (ttt) REVERT: P 35 TRP cc_start: 0.7318 (m100) cc_final: 0.7035 (m100) REVERT: I 103 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8054 (mm-40) REVERT: I 107 ASP cc_start: 0.8731 (m-30) cc_final: 0.8317 (m-30) REVERT: I 368 ASP cc_start: 0.7494 (m-30) cc_final: 0.7152 (m-30) REVERT: I 377 ASN cc_start: 0.8528 (p0) cc_final: 0.8301 (p0) REVERT: I 381 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7779 (mt-10) REVERT: J 588 GLN cc_start: 0.8697 (tp-100) cc_final: 0.8471 (tp-100) REVERT: K 100 ARG cc_start: 0.8188 (mtp-110) cc_final: 0.7603 (ttt180) REVERT: L 20 ARG cc_start: 0.8605 (tpp80) cc_final: 0.8087 (mmt-90) REVERT: L 24 ARG cc_start: 0.8397 (ttm110) cc_final: 0.7967 (ttm110) REVERT: R 97 SER cc_start: 0.9418 (t) cc_final: 0.9151 (t) outliers start: 98 outliers final: 66 residues processed: 561 average time/residue: 0.1620 time to fit residues: 147.5020 Evaluate side-chains 540 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 470 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 41 PRO Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain O residue 41 PRO Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 529 THR Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain Q residue 41 PRO Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 276 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN I 302 ASN K 43 GLN R 26 GLN R 52 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.160412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.115832 restraints weight = 41881.133| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.21 r_work: 0.3309 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 27672 Z= 0.203 Angle : 0.814 16.085 37929 Z= 0.378 Chirality : 0.050 0.471 4707 Planarity : 0.006 0.143 4446 Dihedral : 5.438 58.484 3369 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.38 % Favored : 91.13 % Rotamer: Outliers : 4.94 % Allowed : 18.99 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.15), residues: 3054 helix: 1.25 (0.26), residues: 435 sheet: -0.70 (0.17), residues: 933 loop : -1.71 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 66 TYR 0.019 0.002 TYR E 384 PHE 0.016 0.002 PHE F 592 TRP 0.019 0.001 TRP A 427 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (27435) covalent geometry : angle 0.72930 / 0.36 (37263) SS BOND : bond 0.00629 / 0.44 ( 45) SS BOND : angle 1.30910 / 0.92 ( 90) hydrogen bonds : bond 0.04599 / 3.08 ( 708) hydrogen bonds : angle 5.55693 / 3.84 ( 1836) link_ALPHA1-2 : bond 0.00299 / 0.19 ( 27) link_ALPHA1-2 : angle 1.83246 / 1.30 ( 81) link_ALPHA1-3 : bond 0.00306 / 0.19 ( 21) link_ALPHA1-3 : angle 1.87221 / 1.34 ( 63) link_ALPHA1-6 : bond 0.00333 / 0.22 ( 21) link_ALPHA1-6 : angle 1.51065 / 1.07 ( 63) link_BETA1-4 : bond 0.00611 / 0.48 ( 51) link_BETA1-4 : angle 2.09343 / 1.43 ( 153) link_NAG-ASN : bond 0.00654 / 0.40 ( 72) link_NAG-ASN : angle 4.22842 / 3.07 ( 216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 489 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8756 (tp40) cc_final: 0.8253 (mm-40) REVERT: A 125 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9069 (mp) REVERT: A 161 MET cc_start: 0.8941 (tpp) cc_final: 0.8606 (tpt) REVERT: A 199 SER cc_start: 0.9162 (p) cc_final: 0.8879 (t) REVERT: C 10 GLU cc_start: 0.8707 (pm20) cc_final: 0.8488 (pm20) REVERT: C 100 ARG cc_start: 0.8193 (mtp-110) cc_final: 0.7873 (ttt180) REVERT: D 24 ARG cc_start: 0.8774 (ttm-80) cc_final: 0.8501 (ttm-80) REVERT: M 100 ARG cc_start: 0.8442 (ttt90) cc_final: 0.8182 (tpt-90) REVERT: N 35 TRP cc_start: 0.7884 (m100) cc_final: 0.7575 (m100) REVERT: N 47 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8127 (mm) REVERT: E 168 LYS cc_start: 0.9431 (mmmt) cc_final: 0.9163 (mmtp) REVERT: E 234 ASN cc_start: 0.8350 (m-40) cc_final: 0.8146 (t0) REVERT: G 100 ARG cc_start: 0.8245 (mtp-110) cc_final: 0.7609 (ttt90) REVERT: P 35 TRP cc_start: 0.7535 (m100) cc_final: 0.7165 (m100) REVERT: I 103 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8044 (mm-40) REVERT: I 107 ASP cc_start: 0.8732 (m-30) cc_final: 0.8282 (m-30) REVERT: I 381 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7644 (mt-10) REVERT: K 13 LYS cc_start: 0.8863 (mtpp) cc_final: 0.8562 (mttp) REVERT: K 100 ARG cc_start: 0.8241 (mtp-110) cc_final: 0.7734 (ttt180) REVERT: R 97 SER cc_start: 0.9538 (t) cc_final: 0.9275 (t) outliers start: 133 outliers final: 94 residues processed: 578 average time/residue: 0.1679 time to fit residues: 158.7744 Evaluate side-chains 559 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 463 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 428 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 371 ILE Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain Q residue 41 PRO Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 222 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 296 optimal weight: 10.0000 chunk 231 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 213 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN A 302 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN E 258 GLN P 26 GLN I 92 ASN I 302 ASN R 26 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.161012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.116313 restraints weight = 41724.557| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.20 r_work: 0.3318 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27672 Z= 0.175 Angle : 0.772 15.461 37929 Z= 0.356 Chirality : 0.048 0.404 4707 Planarity : 0.005 0.163 4446 Dihedral : 5.262 44.491 3365 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.69 % Favored : 91.81 % Rotamer: Outliers : 4.31 % Allowed : 20.88 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.15), residues: 3054 helix: 1.16 (0.25), residues: 450 sheet: -0.67 (0.17), residues: 867 loop : -1.68 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 66 TYR 0.019 0.001 TYR R 49 PHE 0.011 0.001 PHE J 592 TRP 0.011 0.001 TRP Q 47 HIS 0.003 0.001 HIS K 100F Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (27435) covalent geometry : angle 0.68793 / 0.34 (37263) SS BOND : bond 0.00660 / 0.46 ( 45) SS BOND : angle 1.43887 / 1.05 ( 90) hydrogen bonds : bond 0.04266 / 2.86 ( 708) hydrogen bonds : angle 5.50728 / 3.79 ( 1836) link_ALPHA1-2 : bond 0.00323 / 0.21 ( 27) link_ALPHA1-2 : angle 1.69943 / 1.21 ( 81) link_ALPHA1-3 : bond 0.00355 / 0.22 ( 21) link_ALPHA1-3 : angle 1.77910 / 1.30 ( 63) link_ALPHA1-6 : bond 0.00324 / 0.21 ( 21) link_ALPHA1-6 : angle 1.48500 / 1.04 ( 63) link_BETA1-4 : bond 0.00377 / 0.25 ( 51) link_BETA1-4 : angle 1.77885 / 1.21 ( 153) link_NAG-ASN : bond 0.00553 / 0.33 ( 72) link_NAG-ASN : angle 4.15853 / 3.01 ( 216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 490 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8765 (m-30) cc_final: 0.8290 (m-30) REVERT: A 161 MET cc_start: 0.8964 (tpp) cc_final: 0.8647 (tpt) REVERT: A 199 SER cc_start: 0.9180 (p) cc_final: 0.8918 (t) REVERT: B 652 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7990 (tp40) REVERT: C 100 ARG cc_start: 0.8187 (mtp-110) cc_final: 0.7785 (ttt180) REVERT: M 97 ARG cc_start: 0.8432 (ttp80) cc_final: 0.8184 (ttp80) REVERT: M 100 ARG cc_start: 0.8423 (ttt90) cc_final: 0.8172 (tpt-90) REVERT: N 47 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8176 (mm) REVERT: N 49 TYR cc_start: 0.7944 (p90) cc_final: 0.7727 (p90) REVERT: E 168 LYS cc_start: 0.9411 (mmmt) cc_final: 0.9197 (mmtp) REVERT: G 86 ASP cc_start: 0.8963 (m-30) cc_final: 0.8677 (m-30) REVERT: G 100 ARG cc_start: 0.8242 (mtp-110) cc_final: 0.7653 (ttt90) REVERT: P 35 TRP cc_start: 0.7511 (m100) cc_final: 0.7213 (m100) REVERT: P 50 ASN cc_start: 0.7786 (t0) cc_final: 0.7578 (t0) REVERT: P 94 ARG cc_start: 0.8863 (mtp180) cc_final: 0.8627 (mmm-85) REVERT: I 103 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8024 (mm-40) REVERT: I 107 ASP cc_start: 0.8743 (m-30) cc_final: 0.8298 (m-30) REVERT: I 381 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7656 (mt-10) REVERT: K 69 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8776 (mm) REVERT: K 100 ARG cc_start: 0.8197 (mtp-110) cc_final: 0.7737 (ttt90) REVERT: L 20 ARG cc_start: 0.8557 (tpp80) cc_final: 0.8344 (tpp-160) REVERT: R 97 SER cc_start: 0.9567 (t) cc_final: 0.9312 (t) outliers start: 116 outliers final: 88 residues processed: 570 average time/residue: 0.1666 time to fit residues: 154.4200 Evaluate side-chains 566 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 475 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 617 LYS Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 95 SER Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 617 LYS Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain Q residue 41 PRO Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 51 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 138 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 239 optimal weight: 0.3980 chunk 249 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 296 optimal weight: 0.0570 chunk 96 optimal weight: 0.6980 chunk 297 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 280 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN E 92 ASN I 92 ASN I 258 GLN I 302 ASN ** Q 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 26 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.159668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.115648 restraints weight = 41420.794| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.19 r_work: 0.3336 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27672 Z= 0.128 Angle : 0.757 22.520 37929 Z= 0.346 Chirality : 0.047 0.529 4707 Planarity : 0.005 0.142 4446 Dihedral : 4.988 36.894 3363 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.60 % Favored : 91.91 % Rotamer: Outliers : 3.60 % Allowed : 22.67 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.15), residues: 3054 helix: 1.29 (0.25), residues: 450 sheet: -0.49 (0.17), residues: 870 loop : -1.62 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 66 TYR 0.015 0.001 TYR A 330 PHE 0.011 0.001 PHE E 233 TRP 0.026 0.001 TRP N 35 HIS 0.004 0.001 HIS I 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (27435) covalent geometry : angle 0.66336 / 0.32 (37263) SS BOND : bond 0.00512 / 0.36 ( 45) SS BOND : angle 1.04348 / 0.76 ( 90) hydrogen bonds : bond 0.03965 / 2.66 ( 708) hydrogen bonds : angle 5.32091 / 3.64 ( 1836) link_ALPHA1-2 : bond 0.00395 / 0.26 ( 27) link_ALPHA1-2 : angle 1.57508 / 1.12 ( 81) link_ALPHA1-3 : bond 0.00438 / 0.28 ( 21) link_ALPHA1-3 : angle 1.69484 / 1.23 ( 63) link_ALPHA1-6 : bond 0.00333 / 0.21 ( 21) link_ALPHA1-6 : angle 1.48157 / 1.05 ( 63) link_BETA1-4 : bond 0.00413 / 0.27 ( 51) link_BETA1-4 : angle 1.60232 / 1.09 ( 153) link_NAG-ASN : bond 0.00624 / 0.35 ( 72) link_NAG-ASN : angle 4.48130 / 3.38 ( 216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 515 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8767 (m-30) cc_final: 0.8299 (m-30) REVERT: A 161 MET cc_start: 0.8975 (tpp) cc_final: 0.8656 (tpt) REVERT: A 199 SER cc_start: 0.9177 (p) cc_final: 0.8889 (t) REVERT: C 100 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7764 (ttt180) REVERT: D 24 ARG cc_start: 0.8676 (ttm-80) cc_final: 0.8383 (ttm-80) REVERT: M 97 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8171 (ttp80) REVERT: M 100 ARG cc_start: 0.8426 (ttt90) cc_final: 0.8169 (tpt-90) REVERT: N 47 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8417 (mm) REVERT: E 201 ILE cc_start: 0.8301 (mp) cc_final: 0.8083 (mm) REVERT: E 377 ASN cc_start: 0.8849 (p0) cc_final: 0.8607 (p0) REVERT: G 86 ASP cc_start: 0.8944 (m-30) cc_final: 0.8619 (m-30) REVERT: G 100 ARG cc_start: 0.8250 (mtp-110) cc_final: 0.7724 (ttt90) REVERT: P 35 TRP cc_start: 0.7493 (m100) cc_final: 0.7246 (m100) REVERT: P 94 ARG cc_start: 0.8818 (mtp180) cc_final: 0.8614 (mmm-85) REVERT: I 103 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8191 (mm-40) REVERT: I 107 ASP cc_start: 0.8784 (m-30) cc_final: 0.8424 (m-30) REVERT: I 164 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8074 (mm-30) REVERT: I 377 ASN cc_start: 0.8778 (p0) cc_final: 0.8516 (p0) REVERT: J 617 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8812 (ptpp) REVERT: K 100 ARG cc_start: 0.8159 (mtp-110) cc_final: 0.7664 (ttt180) REVERT: L 20 ARG cc_start: 0.8536 (tpp80) cc_final: 0.8318 (tpp-160) REVERT: Q 32 TYR cc_start: 0.7228 (p90) cc_final: 0.6733 (p90) REVERT: R 97 SER cc_start: 0.9559 (t) cc_final: 0.9310 (t) outliers start: 97 outliers final: 73 residues processed: 584 average time/residue: 0.1662 time to fit residues: 158.7311 Evaluate side-chains 549 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 474 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 617 LYS Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 244 SER Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 617 LYS Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 51 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 264 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 214 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN F 590 GLN P 26 GLN I 92 ASN I 302 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.159504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.115182 restraints weight = 41880.671| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.20 r_work: 0.3302 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27672 Z= 0.182 Angle : 0.791 23.096 37929 Z= 0.360 Chirality : 0.048 0.492 4707 Planarity : 0.006 0.168 4446 Dihedral : 5.094 41.277 3363 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.60 % Favored : 91.91 % Rotamer: Outliers : 4.16 % Allowed : 22.52 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.15), residues: 3054 helix: 1.22 (0.26), residues: 450 sheet: -0.54 (0.18), residues: 846 loop : -1.61 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 476 TYR 0.017 0.001 TYR N 49 PHE 0.010 0.001 PHE J 592 TRP 0.023 0.001 TRP N 35 HIS 0.005 0.001 HIS N 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (27435) covalent geometry : angle 0.70113 / 0.34 (37263) SS BOND : bond 0.00493 / 0.33 ( 45) SS BOND : angle 1.20817 / 0.89 ( 90) hydrogen bonds : bond 0.04252 / 2.86 ( 708) hydrogen bonds : angle 5.42693 / 3.72 ( 1836) link_ALPHA1-2 : bond 0.00306 / 0.20 ( 27) link_ALPHA1-2 : angle 1.73552 / 1.22 ( 81) link_ALPHA1-3 : bond 0.00303 / 0.19 ( 21) link_ALPHA1-3 : angle 1.79842 / 1.30 ( 63) link_ALPHA1-6 : bond 0.00307 / 0.20 ( 21) link_ALPHA1-6 : angle 1.49988 / 1.06 ( 63) link_BETA1-4 : bond 0.00341 / 0.23 ( 51) link_BETA1-4 : angle 1.68421 / 1.18 ( 153) link_NAG-ASN : bond 0.00580 / 0.35 ( 72) link_NAG-ASN : angle 4.44096 / 3.33 ( 216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 488 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8719 (m-30) cc_final: 0.8242 (m-30) REVERT: A 161 MET cc_start: 0.8986 (tpp) cc_final: 0.8707 (tpp) REVERT: A 181 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8894 (mm) REVERT: A 199 SER cc_start: 0.9202 (p) cc_final: 0.8947 (t) REVERT: B 603 ILE cc_start: 0.9434 (mm) cc_final: 0.9173 (mm) REVERT: C 100 ARG cc_start: 0.8196 (mtp-110) cc_final: 0.7812 (ttt180) REVERT: M 97 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8173 (ttp80) REVERT: M 100 ARG cc_start: 0.8460 (ttt90) cc_final: 0.8210 (tpt-90) REVERT: N 47 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8451 (mm) REVERT: E 377 ASN cc_start: 0.8971 (p0) cc_final: 0.8712 (p0) REVERT: G 86 ASP cc_start: 0.9004 (m-30) cc_final: 0.8715 (m-30) REVERT: G 100 ARG cc_start: 0.8229 (mtp-110) cc_final: 0.7665 (ttt90) REVERT: H 55 LEU cc_start: 0.8541 (tt) cc_final: 0.8274 (tt) REVERT: P 35 TRP cc_start: 0.7610 (m100) cc_final: 0.7220 (m100) REVERT: I 103 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8065 (mm-40) REVERT: I 107 ASP cc_start: 0.8793 (m-30) cc_final: 0.8420 (m-30) REVERT: I 164 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7993 (mm-30) REVERT: I 377 ASN cc_start: 0.8883 (p0) cc_final: 0.8575 (p0) REVERT: K 100 ARG cc_start: 0.8218 (mtp-110) cc_final: 0.7783 (ttt90) REVERT: L 20 ARG cc_start: 0.8561 (tpp80) cc_final: 0.8296 (tpp-160) REVERT: R 97 SER cc_start: 0.9564 (t) cc_final: 0.9332 (t) outliers start: 112 outliers final: 100 residues processed: 561 average time/residue: 0.1684 time to fit residues: 154.8111 Evaluate side-chains 578 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 476 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 617 LYS Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 244 SER Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 617 LYS Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 51 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 97 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 245 optimal weight: 0.0070 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 290 optimal weight: 10.0000 chunk 73 optimal weight: 0.0040 chunk 108 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 overall best weight: 0.5612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN E 92 ASN I 92 ASN I 302 ASN ** Q 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.146148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.107891 restraints weight = 39812.965| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.69 r_work: 0.3115 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27672 Z= 0.124 Angle : 0.745 20.431 37929 Z= 0.340 Chirality : 0.046 0.484 4707 Planarity : 0.005 0.154 4446 Dihedral : 4.951 41.078 3363 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.53 % Favored : 91.98 % Rotamer: Outliers : 3.86 % Allowed : 22.74 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.15), residues: 3054 helix: 1.29 (0.26), residues: 450 sheet: -0.43 (0.18), residues: 843 loop : -1.62 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 476 TYR 0.015 0.001 TYR A 330 PHE 0.007 0.001 PHE O 100K TRP 0.026 0.001 TRP N 96 HIS 0.003 0.001 HIS C 100F Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (27435) covalent geometry : angle 0.66464 / 0.32 (37263) SS BOND : bond 0.00411 / 0.28 ( 45) SS BOND : angle 0.98405 / 0.72 ( 90) hydrogen bonds : bond 0.03863 / 2.60 ( 708) hydrogen bonds : angle 5.26631 / 3.60 ( 1836) link_ALPHA1-2 : bond 0.00403 / 0.26 ( 27) link_ALPHA1-2 : angle 1.56356 / 1.11 ( 81) link_ALPHA1-3 : bond 0.00450 / 0.29 ( 21) link_ALPHA1-3 : angle 1.69188 / 1.23 ( 63) link_ALPHA1-6 : bond 0.00323 / 0.21 ( 21) link_ALPHA1-6 : angle 1.47841 / 1.05 ( 63) link_BETA1-4 : bond 0.00415 / 0.27 ( 51) link_BETA1-4 : angle 1.49996 / 1.04 ( 153) link_NAG-ASN : bond 0.00585 / 0.34 ( 72) link_NAG-ASN : angle 4.10944 / 3.09 ( 216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 497 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8717 (m-30) cc_final: 0.8413 (m-30) REVERT: A 181 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8880 (mm) REVERT: A 199 SER cc_start: 0.9271 (p) cc_final: 0.9011 (t) REVERT: A 475 MET cc_start: 0.7815 (tmm) cc_final: 0.7033 (tmm) REVERT: B 603 ILE cc_start: 0.9398 (mm) cc_final: 0.9167 (mm) REVERT: C 100 ARG cc_start: 0.8268 (mtp-110) cc_final: 0.7989 (ttt180) REVERT: M 97 ARG cc_start: 0.8529 (ttp80) cc_final: 0.8326 (ttp80) REVERT: E 161 MET cc_start: 0.8976 (tpp) cc_final: 0.8730 (tpt) REVERT: F 588 GLN cc_start: 0.8869 (tp40) cc_final: 0.8476 (tt0) REVERT: G 100 ARG cc_start: 0.8210 (mtp-110) cc_final: 0.7769 (ttt90) REVERT: P 35 TRP cc_start: 0.7614 (m100) cc_final: 0.7306 (m100) REVERT: I 103 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8359 (mm-40) REVERT: I 107 ASP cc_start: 0.8858 (m-30) cc_final: 0.8518 (m-30) REVERT: I 164 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8272 (mm-30) REVERT: K 100 ARG cc_start: 0.8216 (mtp-110) cc_final: 0.7793 (ttt180) REVERT: L 20 ARG cc_start: 0.8638 (tpp80) cc_final: 0.8422 (tpp-160) REVERT: Q 29 MET cc_start: 0.5541 (tpt) cc_final: 0.5136 (tpt) REVERT: Q 32 TYR cc_start: 0.7371 (p90) cc_final: 0.6848 (p90) REVERT: Q 100 MET cc_start: 0.8379 (mpp) cc_final: 0.7554 (mpp) outliers start: 104 outliers final: 87 residues processed: 563 average time/residue: 0.1652 time to fit residues: 152.4999 Evaluate side-chains 570 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 482 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 617 LYS Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 617 LYS Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 26 GLN Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 51 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 48 optimal weight: 4.9990 chunk 236 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 276 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN E 302 ASN ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN ** I 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.136431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097161 restraints weight = 39963.537| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.79 r_work: 0.2947 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 27672 Z= 0.247 Angle : 0.841 19.018 37929 Z= 0.387 Chirality : 0.052 0.875 4707 Planarity : 0.006 0.149 4446 Dihedral : 5.302 41.743 3363 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.28 % Favored : 91.36 % Rotamer: Outliers : 4.16 % Allowed : 22.52 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 3054 helix: 1.08 (0.26), residues: 450 sheet: -0.59 (0.17), residues: 864 loop : -1.60 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 166 TYR 0.017 0.002 TYR L 91 PHE 0.014 0.002 PHE I 383 TRP 0.023 0.002 TRP N 35 HIS 0.004 0.001 HIS R 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 (27435) covalent geometry : angle 0.75371 / 0.37 (37263) SS BOND : bond 0.00567 / 0.38 ( 45) SS BOND : angle 1.41442 / 1.04 ( 90) hydrogen bonds : bond 0.04622 / 3.11 ( 708) hydrogen bonds : angle 5.57823 / 3.83 ( 1836) link_ALPHA1-2 : bond 0.00335 / 0.21 ( 27) link_ALPHA1-2 : angle 1.84511 / 1.30 ( 81) link_ALPHA1-3 : bond 0.00231 / 0.15 ( 21) link_ALPHA1-3 : angle 1.87451 / 1.36 ( 63) link_ALPHA1-6 : bond 0.00325 / 0.21 ( 21) link_ALPHA1-6 : angle 1.52085 / 1.08 ( 63) link_BETA1-4 : bond 0.00331 / 0.22 ( 51) link_BETA1-4 : angle 1.86984 / 1.32 ( 153) link_NAG-ASN : bond 0.00648 / 0.42 ( 72) link_NAG-ASN : angle 4.47246 / 3.30 ( 216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 457 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8804 (m-30) cc_final: 0.8547 (m-30) REVERT: A 199 SER cc_start: 0.9323 (p) cc_final: 0.9055 (t) REVERT: A 315 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8982 (mm-40) REVERT: A 475 MET cc_start: 0.8150 (tmm) cc_final: 0.7242 (tmm) REVERT: B 603 ILE cc_start: 0.9539 (OUTLIER) cc_final: 0.9315 (mt) REVERT: C 100 ARG cc_start: 0.8409 (mtp-110) cc_final: 0.8040 (ttt180) REVERT: M 100 ARG cc_start: 0.8653 (ttt90) cc_final: 0.8429 (tpt-90) REVERT: F 588 GLN cc_start: 0.8989 (tp40) cc_final: 0.8588 (tt0) REVERT: G 100 ARG cc_start: 0.8403 (mtp-110) cc_final: 0.7880 (ttt90) REVERT: P 35 TRP cc_start: 0.7852 (m100) cc_final: 0.7483 (m100) REVERT: I 107 ASP cc_start: 0.8983 (m-30) cc_final: 0.8661 (m-30) REVERT: K 100 ARG cc_start: 0.8467 (mtp-110) cc_final: 0.8035 (ttt90) REVERT: L 20 ARG cc_start: 0.8680 (tpp80) cc_final: 0.8387 (tpp-160) REVERT: Q 29 MET cc_start: 0.5644 (tpt) cc_final: 0.5441 (tpt) REVERT: Q 100 MET cc_start: 0.8465 (mpp) cc_final: 0.7595 (mpp) REVERT: R 35 TRP cc_start: 0.7761 (m100) cc_final: 0.7323 (m100) REVERT: R 60 GLU cc_start: 0.8600 (pp20) cc_final: 0.7812 (pp20) outliers start: 112 outliers final: 103 residues processed: 535 average time/residue: 0.1668 time to fit residues: 146.4595 Evaluate side-chains 546 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 442 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 617 LYS Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 244 SER Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 617 LYS Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 13 LYS Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 51 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 280 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 189 optimal weight: 0.0980 chunk 282 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN N 37 GLN E 92 ASN P 50 ASN I 92 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.138866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.100199 restraints weight = 39717.305| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.80 r_work: 0.2992 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27672 Z= 0.152 Angle : 0.776 14.808 37929 Z= 0.360 Chirality : 0.048 0.464 4707 Planarity : 0.005 0.142 4446 Dihedral : 5.255 47.946 3363 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.83 % Favored : 91.72 % Rotamer: Outliers : 3.75 % Allowed : 23.56 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.15), residues: 3054 helix: 1.39 (0.26), residues: 432 sheet: -0.61 (0.18), residues: 852 loop : -1.55 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 298 TYR 0.015 0.001 TYR P 49 PHE 0.008 0.001 PHE A 233 TRP 0.037 0.001 TRP R 96 HIS 0.003 0.001 HIS K 100F Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (27435) covalent geometry : angle 0.69802 / 0.34 (37263) SS BOND : bond 0.00448 / 0.30 ( 45) SS BOND : angle 1.56143 / 1.31 ( 90) hydrogen bonds : bond 0.04229 / 2.87 ( 708) hydrogen bonds : angle 5.46939 / 3.75 ( 1836) link_ALPHA1-2 : bond 0.00379 / 0.25 ( 27) link_ALPHA1-2 : angle 1.63313 / 1.16 ( 81) link_ALPHA1-3 : bond 0.00395 / 0.25 ( 21) link_ALPHA1-3 : angle 1.74722 / 1.26 ( 63) link_ALPHA1-6 : bond 0.00306 / 0.20 ( 21) link_ALPHA1-6 : angle 1.48600 / 1.05 ( 63) link_BETA1-4 : bond 0.00477 / 0.35 ( 51) link_BETA1-4 : angle 1.59422 / 1.10 ( 153) link_NAG-ASN : bond 0.00611 / 0.37 ( 72) link_NAG-ASN : angle 4.02854 / 2.92 ( 216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6927.03 seconds wall clock time: 135 minutes 31.17 seconds (8131.17 seconds total)